“This is a confused approach,” the club said. “Following this logic leads to exactly the opposite of what we all want: staying in the Championship.”
Supporters are angry at how owner Roland Duchatelet is running the club.
A campaigning group called CARD (Coalition Against Roland Duchatelet) want the Belgian to sell his stake in the Addicks, who are 23rd in the Championship, five points adrift of safety.
“Last Sunday, some individuals did not come to the Valley to watch the game and support the team, but came to create disorder on the pitch and interfere with the players and the game,” the statement said.
A mock funeral was held before kick-off while the game was briefly halted when a number of beach balls were thrown on the pitch and some supporters staged a pitch invasion.
Head coach Jose Riga told BBC Radio London he understood the protests but stressed he has a job to do to keep Charlton in the division.
“We still have the chance to make it (Championship survival) happen with the support of the fans until the very last game,” the club’s statement added.
“We must believe it is still possible. Every football fan knows the 12th man is a crucial factor in the success on the pitch.”